5YTI | pdb_00005yti

Crystal structure of flagellar hook associated protein-3 (HAP-3: Q5ZW61_LEGPH) from Legionella pneumophila

PDB DOI: https://doi.org/10.2210/pdb5YTI/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-18 Released: 2018-01-17
Deposition Author(s): Lankipalli, S., Hegde, R.P., Dey, D., Almo, S.C., Ramagopal, U.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.288 (Depositor), 0.279 (DCC)
R-Value Work:
0.235 (Depositor), 0.229 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5YTI

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of hook associated protein-3 (HAP-3: Q5ZW61_LEGPH) from Legionella pneumophila

Lankipalli, S., Ramagopal, U.A.

To be published.

Macromolecule Content

Total Structure Weight: 45.05 kDa
Atom Count: 2,492
Modeled Residue Count: 330
Deposited Residue Count: 411
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook associated protein type 3 FlgL	A	411	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: flgL, lpg1226
UniProt
Find proteins for Q5ZW61 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZW61 Go to UniProtKB: Q5ZW61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZW61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.288 (Depositor), 0.279 (DCC)
R-Value Work: 0.235 (Depositor), 0.229 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.687	α = 90
b = 107.687	β = 90
c = 90.248	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
SHELXDE	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Ramagopal, U.A.

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.